[R-SIG-Mac] Package Installation 'Notes' Question

McGehee, Robert Robert.McGehee at geodecapital.com
Mon Jun 27 22:40:58 CEST 2011

Sorry for the self-reply, however on the second point, I found the culprit. While my R directory was empty except for that one method declaration, I did (accidentally) have the line "Depends: ..., XML" in my description file (copied over from the original package). Since the XML package does have an internal 'updateIds' function, it must be causing the note. And since that function isn't exported, I didn't find it during my search.

CC:ing the XML package maintainer for his interest.

-----Original Message-----
From: McGehee, Robert 
Sent: Monday, June 27, 2011 4:11 PM
To: 'r-sig-mac at r-project.org'
Subject: Package Installation 'Notes' Question

R Mac users,
I have a couple of Mac-specific curiosities regarding package installation that I thought I'd ask the group. 

First, when installing packages on my Mac (and not elsewhere), I see a bunch of lines saying "Note: no visible binding for global variable 'xyz'" (and the like). A Google search on this phrase seemed to indicate that these notes can appear if one sets the _R_CHECK_USE_CODETOOLS_ variable. As I have not done this (and in fact have tried explicitly setting this variable to FALSE), I'm wondering if anyone knows why I get these extra notes on my Mac only.

Second, a note that scrolls by for one package installation that I find particularly unusual is the following:
Note: possible error in 'updateIds(doc, save = x)':
	Unused argument(s) (save = x)

I've managed to whittle down my package into a single method declaration in the R directory that produces this note.

setMethod("Ops", signature("x", "x"), function(e1, e2) {})

However, there is no 'updateIds' function, and I can't seem to find that function anywhere in the R code base (or mine). Does anyone know what this means, and why I get it? Again, I can't seem to reproduce this on my Linux installation, only Mac.

> R.version
platform       x86_64-apple-darwin10.7.0
arch           x86_64
os             darwin10.7.0
system         x86_64, darwin10.7.0
major          2
minor          13.0
year           2011
month          04
day            13
svn rev        55427
language       R
version.string R version 2.13.0 (2011-04-13)

## Here's how I build R, in case that matters.
    $BUILDDIR/R-$RVERS/configure r_arch=x86_64 \
    --prefix="$PREFIX/R/R-${RVERS}" \
    --build=$BUILD \
    --with-x --with-aqua=yes --enable-R-framework=no \
    --with-blas='-framework vecLib' --with-lapack  \
    --x-libraries=/usr/X11/lib --x-includes=/usr/X11/include && \
    make bytecode && \
    make install && \

Robert McGehee, CFA
Geode Capital Management, LLC
One Post Office Square, 28th Floor | Boston, MA | 02109
Direct: (617)392-8396

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